Jorgensen was a close ally with former Yahoo President Susan Decker, who resigned last month after she didn't get the CEO job.

CNBC Silicon Valley Bureau Chief Jim Goldman says Jorgensen's departure is just the first steps of Blatz's highly anticipated reorganization of the company. Goldman says he's been told the new management structure will be about "results," "speed," "accountability," and far more "operationally focused" than the company has been in recent years.

Goldman Blogged: "While Bartz is not announcing which executive will fill what new role at the company yet, I'm told the executives who were offered a chance to stay were told they would now have to figure out whether they want to be part of this new structure, this new company, even if it means a decidedly big reduction in responsibilities for some, and some completely different responsibilities for others. I'm told through a source at Yahoo that when Jorgensen was told this, he and Bartz "mutually decided" that it was time for him to leave the company."